In this study, the soil-millet system in Ping’an District of Qinghai Province was taken as the research object, and the contents of heavy metals and nutrients in soil and millet were determined, and the methods of standard comparison, grading evaluation and principal component analysis were used to evaluate soil quality, identify the nutritional function of millet, and analyze the nutrient sources. The results showed that soil in the study area was alkaline, soil environment quality was good with moderate fertility, and was naturally rich in selenium (Se) with high Ca, Mg, Sr and other natural mineral resources. The heavy metals in millet were far lower than the national limit standards, and there was a synergistic absorption combination sequence of Mg, Mn, Cu, Zn and P in the process of nutrient accumulation. Millet demonstrated a tendency to accumulate Cu, K, Mg, P, Se and Zn elements, and exhibited a strong capacity to transport Cu, Mg, P, Se and Zn. The degree of Fe activation was high while the degree of Cd activation was low in soil. Four nutrient lineages were identified in the nutrient source analysis, which were divided into basic nutrient sources such as Zn, Cu, Mg, Mn, K, and P, fortified nutrient sources such as Fe and Ca, Se functional nutrient source, and Sr functional nutrient source. The high-quality soil environment in the study area cultivates high-quality agricultural products, which are rich in Se, Fe, Cu, Mg, Mn and P, containing vitamin B₁, folic acid, Zn and K. It is a natural functional food for the human body to supplement mineral nutrients such as Se, Fe, Cu, Mg, and Mn, and can be vigorously promoted and applied.